View source: R/graphic_functions.R
plotHaplotype | R Documentation |
The plotHaplotype
functions visualizes an inferred haplotype.
plotHaplotype( hap_table, html_output = FALSE, genes_order = NULL, text_size = 14, removeIGH = TRUE, plotYaxis = TRUE, chain = c("IGH", "IGK", "IGL", "TRB"), dir )
hap_table |
haplotype summary table. See details. |
html_output |
if TRUE, a html5 interactive graph is outputed. Default is FALSE. |
genes_order |
A vector of the genes by the desired order. Default is by GENE.loc |
text_size |
the size of graph labels. Default is 14 (pts). |
removeIGH |
if TRUE, 'IGH'\'IGK'\'IGL'\'TRB' prefix is removed from gene names. |
plotYaxis |
if TRUE, Y axis labels (gene names) are plotted on the middle and right plots. Default is TRUE. |
chain |
the Ig/TR chain: IGH,IGK,IGL,TRB. Default is IGH. |
dir |
The output folder for saving the haplotype map for multiple individuals. |
A data.frame
in a haplotype format created by createFullHaplotype
function.
A haplotype map visualization. If more than one subject is visualized, a pdf is created. If html_output is TRUE, a folder named html_output is created with individual graphs.
# Selecting a single individual from the haplotype samples data haplo_db = samplesHaplotype[samplesHaplotype$subject=='I5', ] # plot haplotype plotHaplotype(haplo_db)
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